R help - Oct 2009 - how to draw stacked ellipses to illustrate the shared and specific of multiple objects using R

Dear R-help listers,

I am now asking for helps on how to draw stacked ellipses to
illustrate the shared and specific of multiple objects using R.

My problem comes from my population genetics study. Now, I genotyped
three species, and I get known about the amount of shared and specific
haplotypes in each of the species and their combinations. I want to
illustrate this result in three stack ellipses, with the shared and
unique area of the stack ellipses were annotated with the relative
amount.

 my data is as followed:

------------------------------------------------------------
hap.type	hap.dis.num	hap.dis.per	types
hap.Pd	8	27.5862069	Pd specific
hap.Pt	6	20.68965517	Pt specific
hap.Py	9	31.03448276	Py specific
hap.PdPt	3	10.34482759	PdPt shared
hap.PdPy	3	10.34482759	PdPy shared
hap.PtPy	0	0	PtPy shared
hap.3P	0	0	3 species shared
-------------------------------------------------------------

Several individuals of 3 species (Pd, Pt, Py) were genotyped, the
summary of haplotype distribution in species level were contained in
the forward dataset.

Could you please give any direction on this graphical problem? Thank
you in advance.

Best regards,

Mao J-F

On 10/20/2009 06:10 PM, Mao Jianfeng wrote:
> Dear R-help listers,
>
> I am now asking for helps on how to draw stacked ellipses to
> illustrate the shared and specific of multiple objects using R.
>
> My problem comes from my population genetics study. Now, I genotyped
> three species, and I get known about the amount of shared and specific
> haplotypes in each of the species and their combinations. I want to
> illustrate this result in three stack ellipses, with the shared and
> unique area of the stack ellipses were annotated with the relative
> amount.
>
>   my data is as followed:
>
> ------------------------------------------------------------
> hap.type	hap.dis.num	hap.dis.per	types
> hap.Pd	8	27.5862069	Pd specific
> hap.Pt	6	20.68965517	Pt specific
> hap.Py	9	31.03448276	Py specific
> hap.PdPt	3	10.34482759	PdPt shared
> hap.PdPy	3	10.34482759	PdPy shared
> hap.PtPy	0	0	PtPy shared
> hap.3P	0	0	3 species shared
> -------------------------------------------------------------
>
> Several individuals of 3 species (Pd, Pt, Py) were genotyped, the
> summary of haplotype distribution in species level were contained in
> the forward dataset.
>
> Could you please give any direction on this graphical problem? Thank
> you in advance.
>    
Hi Mao,
I can't help you with ellipses, but intersectDiagram in the plotrix 
package may do what you want in a different way. Try this:

library(plotrix)
hapIntList<-
 
getIntersectList(3,xnames=c("hap.Pd","hap.Pt","hap.Py"))
# enter the data as follows
#Number of elements in hap.Pd - 1: 27.586
#Number of elements in hap.Pt - 1: 20.689
#Number of elements in hap.Py - 1: 31.034
#Number of elements in hap.Pdhap.Pt - 1: 10.345
#Number of elements in hap.Pdhap.Py - 1: 10.345
#Number of elements in hap.Pthap.Py - 1: 0
#Number of elements in hap.Pdhap.Pthap.Py - 1: 0
#Total number of elements - 1: 99.999
# this is a small bug that I have fixed and will
# not be necessary from v2.7-2 onward
class(hapIntList)<-"intersectList"
intersectDiagram(hapIntList)

I'm quite interested in whether this is of any use to you, as I had not 
even thought of this particular use for intersectDiagram.

Jim